2(A)-(D): Analysis of pathway activity and intrinsic subtypes

2(A): TCGA BRCA all pathway

## Loading required package: gplots
## 
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
## 
##     lowess
## Loading required package: RColorBrewer
## Loading required package: data.table
## Loading required package: mclust
## Package 'mclust' version 5.1
## Type 'citation("mclust")' for citing this R package in publications.
## Loading required package: ggplot2
## Loading required package: gridExtra
## Warning: package 'gridExtra' was built under R version 3.2.4
## Loading required package: devtools
## Loading required package: grid
## Loading required package: cluster
## 
Read 42.8% of 23368 rows
Read 85.6% of 23368 rows
Read 23368 rows and 1120 (of 1120) columns from 0.361 GB file in 00:00:04

2(B): ICBP all pathways

2(C): TCGA, k-means of 4 pathways

2(D): ICBP, k-means of 4 pathways

3(A)-(C): Unsupervised variance analysis confirms the significance of the GFRN phenotypes

Perform Principal Component Analysis in ICBP cell lines

## [1] "Proportion of variance contributed by first 5 principal components in ICBP gene expression data: 0.427196248976044"

3(A): Principal Component Analysis in TCGA BRCA

## [1] "Proportion of variance contributed by first 5 principal components in TCGA BRCA gene expression data: 0.343182614266816"

3(B): Boxplot TCGA Principal Components across clinical subtypes (IHC: ER, PR, HER2)

3(C) Correlate TCGA Principal Components with ASSIGN generated GFRN pathway predictions

4(A)-(E):Survival and growth phenotypes express dichotomous cell survival mechanism

4(A):Heatmap of breast cancer cell lines from Western Blot

4(C)-(E): Gene and protein expression are significantly different between growth and survival phenotypes

## [1] "733 names have been changed"
## [1] "analyzing BIM"
## [1] "BIM data available"

## [1] "analyzing BAD"
## [1] "BAD data available"

## [1] "analyzing MCL1"

5(A) &(B): Growth factor network phenotypes reflect dichotomous drug response in breast cancer cell lines

5(A): Correlate ICBP GFRN pathway predictions with ICBP drug response and make Heatmap

5(B): Correlate GFRN pathway predictions with drug response in an independent drug assay and make Heatmap

Supplemental Figures 3(A)-(H):

Protein based pathway validations codes are in ./ASSIGN folder. Gene expression, mutation and IHC-based validations are shown here.

## [1] "757 names have been changed"

Supplemental Figures 4(A)-(G): Boxplot GFRN pathway activity across breast cancer clinical subtypes (IHC)

Supplemental Figures 5(A)-(G): Boxplot GFRN pathway activity across breast cancer intrinsic subtypes (PAM50)

## [1] "517 names have been changed"

Supplemental Figure 6(A)&(B): Boxplot TCGA Principal Components across BRCA intrinsic subtypes (PAM50)

## [1] "Spearman correlation of PC1 and mean gene expression of each sample:  -0.786414519142557"

Supplemental Figures 7(A)-(D):

This analysis was run on Thu Jun 30 10:33:28 2016